We also have a stage box expansion unit. So we are running 50 in puts but not all are visible when I select input on the desk top. The question is why do I not see all the inputs or how can I add the ones I don't see?
The Expression 3 is capable of mixing 66 inputs total, so you're still within your limits.
The layers default to a standard setup of input channels (A), Stereo input & FX return channels (B), Mixes (C), and Matrices (D)...mostly; there's some crossover here and there.
If you go into the Fader Options and select a particular fader, you can choose what it's associated with - layer, mono input channel, stereo input channel, mix, matrix.
If the stage box is not immediately recognized, you have to reset the configuration on the console to make it appear as a selectable I
input. Have you scrolled past all of the inputs to see if the MADI inputs are available? What option card do you have installed?